Re: [Bioc-devel] Bioc Git credentials

eys if you don’t have the old key pairs. > > > > Best, > > > > Nitesh > > > > *From: *Bioc-devel on behalf of > Leonard Goldstein > *Date: *Sunday, May 2, 2021 at 10:06 PM > *To: *bioc-devel@r-project.org > *Subject: *[Bioc-devel] Bioc Git credentials

[Bioc-devel] Bioc Git credentials

Hi, I'm maintaining the SGSeq Bioc package and recently changed the maintainer email address. I'm trying to activate a new account for Git credentials here , but get the following error message: ldgoldst...@gmail.com is not associa

Re: [Bioc-devel] BSgenome changes

; > > > > > > Thanks again for the explanation. > > > > > > Cheers, > > > Felix > > > > > > -Ursprüngliche Nachricht- > > > Von: Bioc-devel > <mailto:bioc-devel-

[Bioc-devel] BSgenome changes

Dear Bioc team, I'm following up on this recent GitHub issue . Please see the issue for more details and code examples. It looks like changes in Bioc devel result in two copies of the mitochondrial chromosome for BSgenome.Hsapiens.UCSC.hg19 -- one named ch

Re: [Bioc-devel] Bioc-devel changes and SummarizedExperiment class

Thanks Hervé! Leonard On Tue, Apr 10, 2018 at 11:03 AM, Hervé Pagès wrote: > Hi Leonard, > > This should be fixed in SGSeq 1.13.6 (see commit > 5dc16968f7ea1a4b59595ebaabacca9a76699b80). > > Cheers, > H. > > > On 04/04/2018 09:23 AM, Leonard Goldstein wrote: &g

[Bioc-devel] Bioc-devel changes and SummarizedExperiment class

Hi Hervé, Some recent changes in bioc-devel are causing trouble with SummarizedExperiment objects if the rowRanges slot inherits from GRangesList. Please see example below. Thanks in advance for your help. Leonard -- > library(SGSeq) > > ## SGVariants object inherits from GRangesList > is(sgv

Re: [Bioc-devel] exonsBy dropping genes from TxDb

Thanks Hervé and others for looking into this. Leonard On Sun, Oct 29, 2017 at 10:19 PM, Hervé Pagès wrote: > Thanks Dario and Mike for looking into this. > > In the mean time I added makeTxDbFromEnsembl() for creating a TxDb > object by querying directly an Ensembl MySQL server. Only lightly >

[Bioc-devel] exonsBy dropping genes from TxDb

Dear bioc-devel, I noticed exonsBy is dropping a lot of genes when run on a TxDb object created with makeTxDbFromBiomart (see below). Please also see related post on the Bioconductor support site: https://support.bioconductor.org/p/101951/#102160 Thanks for your help. Leonard -- > tx <- makeTx

Re: [Bioc-devel] Changes S4Vectors etc.

anges" "Rsamtools" > [4] "SummarizedExperiment" "AnnotationDbi""Biostrings" > [7] "GenomicAlignments""GenomicFeatures" "GenomeInfoDb" > [10] "rtracklayer" "XVector&qu

[Bioc-devel] Changes S4Vectors etc.

Hi Hervé, It looks like there have been some changes in bioc-devel (S4Vectors etc.) that break the SGSeq package (see below). I'm not sure whether this is something that needs to be addressed in SGSeq or its dependencies. I'd be grateful for any pointers. Thanks for your help. Leonard -- > examp

Re: [Bioc-devel] Bug in setdiff() for signature 'IRangesList, IRangesList'?

Thanks Michael! Leonard On Mon, Nov 7, 2016 at 11:35 AM, Michael Lawrence wrote: > I fixed this in 2.9.6 and 2.8.1. > > It brings to light an interesting pecularity of the recycling rule. > > Thanks, > Michael > > On Mon, Nov 7, 2016 at 9:46 AM, Leonard Goldstein >

[Bioc-devel] Bug in setdiff() for signature 'IRangesList, IRangesList'?

Dear Hervé et al. I noticed that setdiff(x, y) where 'x' is an IRangesList containing an empty IRanges results in an error (see below). I would have expected the function to return the IRangesList with an empty IRanges? Many thanks for your help. Leonard -- > x <- IRangesList(IRanges()) > y <-

Re: [Bioc-devel] New argument 'use.names' in granges() function

them like >> 'use.names', 'use.mcols', 'ignore.strand' etc.. >> That makes the code a lot more readable. >> >> Cheers, >> H. >> >> >> On 06/16/2016 04:46 PM, Leonard Goldstein wrote: >> >>> Hi Hervé, &

[Bioc-devel] New argument 'use.names' in granges() function

Hi Hervé, I noticed a recent change in the release and development version of GenomicRanges, which introduces a new argument 'use.names' for granges() and other functions. The change breaks the SGSeq package, since it uses granges() relying on positional argument matching (and 'use.names' has bee

Re: [Bioc-devel] segfault when using RleList in DataFrames

th core dump, if enabled) > 2: normal R exit > 3: exit R without saving workspace > 4: exit R saving workspace > Selection: 2 > Save workspace image? [y/n/c]: > > It is now fixed in release (S4Vectors 0.8.4 and IRanges 2.4.5) and > devel (S4Vectors 0.9.12 and IRanges 2.5.10

[Bioc-devel] segfault when using RleList in DataFrames

Hi all, I ran into problems when using an RleList as column in a DataFrame object (see example below). Many thanks in advance for your help. Leonard > sessionInfo() R version 3.2.2 (2015-08-14) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux Server release 6.6 (S

Re: [Bioc-devel] error when combining objects inheriting from GRangesList

Hi Hervé, OK thanks for the workaround and the quick reply. Best wishes, Leonard On Fri, Dec 4, 2015 at 10:41 AM, Hervé Pagès wrote: > Hi Leonard, > > > On 12/04/2015 09:43 AM, Leonard Goldstein wrote: >> >> Hi all, >> >> In the latest Bioc release (an

[Bioc-devel] error when combining objects inheriting from GRangesList

Hi all, In the latest Bioc release (and devel) I encountered problems with classes inheriting from GRangesList. Combining two or more objects that belong to such classes can result in an error, as the combined object is apparently not recognized as a valid instance of the class. I included an exam

Re: [Bioc-devel] S4 classes extending GRangesList

class as its 1st argument. > > Thanks for your patience and for the reminder. > H. > > > On 09/29/2015 10:35 AM, Leonard Goldstein wrote: >> >> Hi Hervé, >> >> This still looks broken in the current bioc-devel. Just wanted to >> follow up in case it got miss

Re: [Bioc-devel] S4 classes extending GRangesList

Hi Hervé, This still looks broken in the current bioc-devel. Just wanted to follow up in case it got missed. Thanks again. Leonard On Thu, Jun 11, 2015 at 11:59 AM, Leonard Goldstein wrote: > Thanks Hervé. > > Best wishes, > > Leonard > > > On Thu, Jun 11, 2015

Re: [Bioc-devel] using covr with the parallel package

t; On Mon, Aug 17, 2015 at 11:24 AM, Jim Hester >> wrote: >> > Leonard, >> > >> > Can you link to an example where this behavior is occurring? I can see >> > evidence where the coverage is working as expected when using mclapply, >> > e.g. >>

[Bioc-devel] using covr with the parallel package

Hi Jim, I noticed that when covr calculates test coverage, functions called inside mclapply or mcmapply with argument mc.preschedule = FALSE are considered untested (even if unit tests exist) When running checks I only use one core. So an easy fix would be to set mc.preschedule to TRUE if mc.core

Re: [Bioc-devel] error using the DEXSeqDataSet function

ibbioc_1.15.0 munsell_0.4.2 > [19] gtable_0.1.2 futile.logger_1.4.1 hwriter_1.3.2 > [22] latticeExtra_0.6-26 geneplotter_1.47.0 biomaRt_2.25.1 > [25] proto_0.3-10 acepack_1.3-3.3 xtable_1.7-4 > [28] scales_0.2.5 Hmisc_3.16-0 annotate_1.47.4 > [31]

[Bioc-devel] error using the DEXSeqDataSet function

Hi all, I'm having trouble creating a DEXSeqDataSet object (in the devel version of DEXSeq) Running the example included in the manual page results in the same error I get with my own data (see below) Many thanks for your help. Leonard > library(DEXSeq) > countData <- matrix( rpois(1, 100)

Re: [Bioc-devel] S4 classes extending GRangesList

Thanks Hervé. Best wishes, Leonard On Thu, Jun 11, 2015 at 10:58 AM, Hervé Pagès wrote: > Hi Leonard, > > It's a bug in the "c" method for "CompressedList" object. I'll fix > that. Thanks for the report. > > H. > > > On 06/11/2015

[Bioc-devel] S4 classes extending GRangesList

Hi all, I noticed that when combining instances of a class that inherits from GRangesList, the result does not preserve the class (it is returned as a GRangesList instead). The class is preserved in other situations (e.g. when a class extends GRanges). See below for an example. Is there a reason w

Re: [Bioc-devel] scanBam() segfault error

AM, Martin Morgan wrote: >> >> On 04/17/2015 08:59 AM, Leonard Goldstein wrote: >>> >>> Hi all, >>> >>> I ran into a segfault error when trying to read paired-end RNA-seq >>> alignments with scanBam (see below). This seems to be a problem >>

[Bioc-devel] scanBam() segfault error

Hi all, I ran into a segfault error when trying to read paired-end RNA-seq alignments with scanBam (see below). This seems to be a problem introduced in Rsamtools version 1.19.35 (1.19.34 works fine). In case you need the BAM file for testing, please let me know. Many thanks for your help. Leonar

Re: [Bioc-devel] BamTallyParam argument 'which'

ng out alignments from a SAM/BAM, and deriving a > summary (tallyVariants) from a BAM. It seems like an argument could be made > for a tally set to not contain duplicates. > > On Mon, Feb 23, 2015 at 11:05 AM, Leonard Goldstein > wrote: >> >> Hi Michael and Thomas, >>

Re: [Bioc-devel] BamTallyParam argument 'which'

Hi Michael and Thomas, I ran into the same problem in the past (i.e. when I started working with functions like scanBam I expected them not to return the same alignment multiple times) One thing to consider might be that returning alignments multiple times is consistent with the behavior of the s

Re: [Bioc-devel] Error when reading BAM files with readGAlignmentPairs

ATEST/GenomicAlignments/zin2-buildsrc.html > > This is a known issue that is the consequence of a recent change in > Rsamtools. We'll sort it out. > > Thanks for your patience, > H. > > > > On 12/12/2014 12:51 PM, Leonard Goldstein wrote: >> >> Dear Bioc

[Bioc-devel] Error when reading BAM files with readGAlignmentPairs

Dear Bioc developers, There seems to be an issue with GenomicAlignments or dependent packages as I can no longer read BAM files with readGAlignmentPairs that could be read without problems previously (see example below). I assume this is a general problem but can provide test files if necessary.

[Bioc-devel] flank function with start argument a named vector

Dear Bioc developers, I ran into problems when using the flank function with the start argument set to a named vector. This returns an IRanges with named starts and ends, which causes problems downstream. Please see example below. Thanks for your help Leonard > ir <- IRanges(1, 1) > fl <- fla

Re: [Bioc-devel] readGAlignmentPairs function broken?

imings but I suspect this >> transformation is taking a little bit too long and there might be room >> for optimization (like e.g. avoiding the GAlignmentsList intermediate >> representation). >> >> I'll keep you updated. >> >> Thanks, >> H. &g

Re: [Bioc-devel] readGAlignmentPairs function broken?

In the mean time > you can grab it directly from svn: > > > https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicAlignments > > Please let me know if you still run into problems with this. > Thanks! > > > H. > > On 12/19/2013 10:41 AM, Leonard Gold

Re: [Bioc-devel] readGAlignmentPairs function broken?

Hi Hervé You probably spotted this already but it looks like the problem is introduced between GenomicAlignments revisions r84052 (0.99.8) and r84106 (0.99.9) Best wishes Leonard On Wed, Dec 18, 2013 at 5:25 PM, Leonard Goldstein wrote: > Dear list, > > There seems to be a problem

[Bioc-devel] readGAlignmentPairs function broken?

Dear list, There seems to be a problem with the readGAlignmentPairs function: Querying genomic regions without any alignments using the which argument results in an error -- see (1) below. Reading in a whole chromosome takes indefinitely (or at least much longer than in previous versions) -- see